tbuckley/cabot-search huggingface dataset:
Accuracy of a smartphone application for blood pressure estimation in Bangladesh, South Africa, and Tanzania
Authors: Charles Festo, Valerie Vannevel, Hasmot Ali, Tigest Tamrat, Getrud J. Mollel, Tsakane Hlongwane, Kaniz A. Fahmida, Kelsey Alland, María Barreix, Hedieh Mehrtash, Ronaldo Silva, Soe Soe Thwin, Garrett Mehl, Alain B. Labrique, Honorati Masanja, Ӧzge Tunçalp
Journal: npj Digital Medicine (2023)

Undetected and unmonitored hypertension carries substantial mortality and morbidity, especially during pregnancy. We assessed the accuracy of OptiBPTM, a smartphone application for estimating blood pressure (BP), across diverse settings. The study was conducted in community settings: Gaibandha, Bangladesh and Ifakara, Tanzania for general populations, and Kalafong Provincial Tertiary Hospital, South Africa for pregnant populations. Based on guidance from the International Organization for Standardization (ISO) 81,060-2:2018 for non-invasive BP devices and global consensus statement, we compared BP measurements taken by two independent trained nurses on a standard auscultatory cuff to the BP measurements taken by a research version of OptiBPTM called CamBP. For ISO criterion 1, the mean error was 0.5 ± 5.8 mm Hg for the systolic blood pressure (SBP) and 0.1 ± 3.9 mmHg for the diastolic blood pressure (DBP) in South Africa; 0.8 ± 7.0 mmHg for the SBP and -0.4 ± 4.0 mmHg for the DBP in Tanzania; 3.3 ± 7.4 mmHg for the SBP and -0.4 ± 4.3 mmHg for the DBP in Bangladesh. For ISO criterion 2, the average standard deviation of the mean error per subject was 4.9 mmHg for the SBP and 3.4 mmHg for the DBP in South Africa; 6.3 mmHg for the SBP and 3.6 mmHg for the DBP in Tanzania; 6.4 mmHg for the SBP and 3.8 mmHg for the DBP in Bangladesh. OptiBPTM demonstrated accuracy against ISO standards in study populations, including pregnant populations, except in Bangladesh for SBP (criterion 2). Further research is needed to improve performance across different populations and integration within health systems.
Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
Authors: Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan
Journal: Genome biology (2023)

We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that map to multiple genome locations or across splice boundaries and can consider various types of background in the estimation of read enrichment. By applying RCRUNCH to the eCLIP data from the ENCODE project, we have constructed a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates the reproducible analysis of CLIP data, enabling studies of post-transcriptional control of gene expression.
DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
Authors: Longxian Chen, Liang Ou, Xinyun Jing, Yimeng Kong, Bingran Xie, Niubing Zhang, Han Shi, Hang Qin, Xuan Li, Pei Hao
Journal: Genome biology (2023)

Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective.
GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species
Authors: Liubin Zhang, Yangyang Yuan, Wenjie Peng, Bin Tang, Mulin Jun Li, Hongsheng Gui, Qiang Wang, Miaoxin Li
Journal: Genome biology (2023)

Abstract Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC’s data structure and algorithms are valuable for accelerating large-scale genomic research.
Comutations and KRASG12C Inhibitor Efficacy in Advanced NSCLC
Authors: Marcelo V. Negrao, Haniel A. Araujo, Giuseppe Lamberti, Alissa J. Cooper, Neal S. Akhave, Teng Zhou, Lukas Delasos, J. Kevin Hicks, Mihaela Aldea, Gabriele Minuti, Jacobi Hines, Jacqueline V. Aredo, Michael J. Dennis, Turja Chakrabarti, Susan C. Scott, Paolo Bironzo, Matthias Scheffler, Petros Christopoulos, Albrecht Stenzinger, Jonathan W. Riess, So Yeon Kim, Sarah B. Goldberg, Mingjia Li, Qi Wang, Yun Qing, Ying Ni, Minh Truong Do, Richard Lee, Biagio Ricciuti, Joao Victor Alessi, Jing Wang, Blerina Resuli, Lorenza Landi, Shu-Chi Tseng, Mizuki Nishino, Subba R. Digumarthy, Waree Rinsurongkawong, Vadeerat Rinsurongkawong, Ara A. Vaporciyan, George R. Blumenschein, Jianjun Zhang, Dwight H. Owen, Collin M. Blakely, Giannis Mountzios, Catherine A. Shu, Christine M. Bestvina, Marina Chiara Garassino, Kristen A. Marrone, Jhanelle E. Gray, Sandip Pravin Patel, Amy L. Cummings, Heather A. Wakelee, Juergen Wolf, Giorgio Vittorio Scagliotti, Federico Cappuzzo, Fabrice Barlesi, Pradnya D. Patil, Leylah Drusbosky, Don L. Gibbons, Funda Meric-Bernstam, J. Jack Lee, John V. Heymach, David S. Hong, Rebecca S. Heist, Mark M. Awad, Ferdinandos Skoulidis
Journal: Cancer Discovery (2023)

Molecular modifiers of KRASG12C inhibitor (KRASG12Ci) efficacy in advanced KRASG12C-mutant NSCLC are poorly defined. In a large unbiased clinicogenomic analysis of 424 patients with non-small cell lung cancer (NSCLC), we identified and validated coalterations in KEAP1, SMARCA4, and CDKN2A as major independent determinants of inferior clinical outcomes with KRASG12Ci monotherapy. Collectively, comutations in these three tumor suppressor genes segregated patients into distinct prognostic subgroups and captured ∼50% of those with early disease progression (progression-free survival ≤3 months) with KRASG12Ci. Pathway-level integration of less prevalent coalterations in functionally related genes nominated PI3K/AKT/MTOR pathway and additional baseline RAS gene alterations, including amplifications, as candidate drivers of inferior outcomes with KRASG12Ci, and revealed a possible association between defective DNA damage response/repair and improved KRASG12Ci efficacy. Our findings propose a framework for patient stratification and clinical outcome prediction in KRASG12C-mutant NSCLC that can inform rational selection and appropriate tailoring of emerging combination therapies. In this work, we identify co-occurring genomic alterations in KEAP1, SMARCA4, and CDKN2A as independent determinants of poor clinical outcomes with KRASG12Ci monotherapy in advanced NSCLC, and we propose a framework for patient stratification and treatment personalization based on the comutational status of individual tumors. See related commentary by Heng et al., p. 1513. This article is highlighted in the In This Issue feature, p. 1501.
Endoscopic ultrasound-guided choledochoduodenostomy using a drill dilator
Authors: Takeshi Okamoto, Tsuyoshi Takeda, Naoki Sasahira
Journal: Endoscopy (2023)

Use of the Tornus ES drill dilator (Asahi Intecc Co., Ltd., Aichi, Japan) has been reported for tract dilation in various settings [1] [2] [3] [4] [5]. While it has been used successfully in endoscopic ultrasound (EUS)-guided hepaticogastrostomy, tract dilation in EUS-guided choledochoduodenostomy (CDS) can be even more challenging [1] [2] [3]. The bile duct is visualized directly under the probe and the portal vein runs parallel on the other side, making large strokes dangerous. Extrahepatic bile ducts can be extremely stiff, particularly during conversion from conventional transpapillary stenting, precluding the insertion of mechanical or balloon dilators and requiring high-risk tract dilation using electrocautery. We report successful tract dilation in EUS-CDS using the Tornus ES dilator.
Botryoid rhabdomyosarcoma or parasites: transnasal choledoscopy as a diagnostic tool
Authors: Gül Şeker, Mesut Akarsu, Yunus Güler, Özlem Gülpınar Aydın, Safiye Günden Aktaş, Yeşim Öztürk
Journal: Endoscopy (2023)

A 5-year-old girl presented with jaundice and loss of appetite. Physical examination revealed that she had a palpable liver 4 cm below the right costal arch. There were no ascites, cervical adenopathy, or splenomegaly. Laboratory values showed elevated liver enzymes and direct bilirubin.
Balloon-assisted technique for endoscopic en bloc retrieval of a large gastric gastrointestinal stromal tumor specimen
Authors: Suhua Wu, Song He, Zhechuan Mei, Feng Xu, Xiaodong Guo, Yingchi Zhang, Chao Deng
Journal: Endoscopy (2023)

A 64-year-old woman underwent gastroscopy and abdominal computed tomography, which revealed a 4.0 × 3.5 cm gastric gastrointestinal stromal tumor (GIST) in the anterior wall of the stomach ([Fig. 1 a]). After full evaluation, an endoscopic full-thickness resection technique was used to achieve complete resection ([Fig. 1 b]). It is very important to retrieve the complete specimen to allow for subsequent pathological evaluation; however, retrieval is difficult for specimen larger than 3.5 cm. Wu et al. successfully applied a balloon-assisted technique for removal of large esophageal foreign bodies [1]. Therefore, we applied this technique for endoscopic en bloc retrieval of a large gastric GIST specimen ([Video 1]).
Safety of Real-life Usage of Advanced Hybrid Closed-Loop System MiniMed 780G in Children With Type 1 Diabetes Younger Than 7 Years Old
Authors: Gianluca Tornese, Claudia Carletti, Maria Andrea Lanzetta, Gianluca Tamaro, Egidio Barbi, Elena Faleschini
Journal: Diabetes Care (2023)

Table 1-Sensor-specific measures of glycemic control, adherence to advanced hybrid closed loop (a-HCL) use, insulin dose and basal-to-bolus ratio
Diagnostic yield of genetic screening in a diverse, community-ascertained cohort
Authors: Nandana D. Rao, Jailanie Kaganovsky, Emily A. Malouf, Sandy Coe, Jennifer Huey, Darwin Tsinajinne, Sajida Hassan, Kristine M. King, Stephanie M. Fullerton, Annie T. Chen, Brian H. Shirts
Journal: Genome Medicine (2023)

Population screening for genetic risk of adult-onset preventable conditions has been proposed as an attractive public health intervention. Screening unselected individuals can identify many individuals who will not be identified through current genetic testing guidelines.We sought to evaluate enrollment in and diagnostic yield of population genetic screening in a resource-limited setting among a diverse population. We developed a low-cost, short-read next-generation sequencing panel of 25 genes that had 98.4% sensitivity and 99.98% specificity compared to diagnostic panels. We used email invitations to recruit a diverse cohort of patients in the University of Washington Medical Center system unselected for personal or family history of hereditary disease. Participants were sent a saliva collection kit in the mail with instructions on kit use and return. Results were returned using a secure online portal. Enrollment and diagnostic yield were assessed overall and across race and ethnicity groups.Overall, 40,857 people were invited and 2889 (7.1%) enrolled. Enrollment varied across race and ethnicity groups, with the lowest enrollment among African American individuals (3.3%) and the highest among Multiracial or Other Race individuals (13.0%). Of 2864 enrollees who received screening results, 106 actionable variants were identified in 103 individuals (3.6%). Of those who screened positive, 30.1% already knew about their results from prior genetic testing. The diagnostic yield was 74 new, actionable genetic findings (2.6%). The addition of more recently identified cancer risk genes increased the diagnostic yield of screening.Population screening can identify additional individuals that could benefit from prevention, but challenges in recruitment and sample collection will reduce actual enrollment and yield. These challenges should not be overlooked in intervention planning or in cost and benefit analysis.
HBV DNA Integration into Telomerase or MLL4 Genes and TERT Promoter Point Mutation as Three Independent Signatures in Subgrouping HBV-Related HCC with Distinct Features
Authors: Chiao-Ling Li, Chia-Lang Hsu, You-Yu Lin, Ming-Chih Ho, Ray-Heng Hu, Chi-Ling Chen, Tung-Ching Ho, Yung-Feng Lin, Shih-Feng Tsai, Sheng-Tai Tzeng, Chin-Fang Huang, Ya-Chun Wang, Shiou-Hwei Yeh, Pei-Jer Chen
Journal: Liver Cancer (2023)

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; A set of genetic mutations to classify hepatocellular carcinoma (HCC) useful to clinical studies is an unmet need. Hepatitis B virus-related HCC (HBV-HCC) harbors a unique genetic mutation, namely, the HBV integration, among other somatic endogenous gene mutations. We explored a combination of HBV DNA integrations and common somatic mutations to classify HBV-HCC by using a capture-sequencing platform. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; A total of 153 HBV-HCCs after surgical resection were subjected to capture sequencing to identify HBV integrations and three common somatic mutations in genomes. Three mutually exclusive mutations, HBV DNA integration into the TERT promoter, HBV DNA integration into MLL4, or TERT promoter point mutation, were identified in HBV-HCC. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; They were used to classify HBV-HCCs into four groups: G1 with HBV-TERT integration (25.5%); G2 with HBV-MLL4 integration (10.5%); G3 with TERT promoter mutation (30.1%); and G4 without these three mutations (34.0%). Clinically, G3 has the highest male-to-female ratio, cirrhosis rate, and associated with higher early recurrence and mortality after resection, but G4 has the best outcome. Transcriptomic analysis revealed a grouping different from the published ones and G2 with an active immune profile related to immune checkpoint inhibitor response. Analysis of integrated HBV DNA provided clues for HBV genotype and variants in carcinogenesis of different HCC subgroup. This new classification was also validated in another independent cohort. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; A simple and robust genetic classification was developed to aid in understanding HBV-HCC and in harmonizing clinical studies.
Successful removal of a proximally migrated pancreatic stent using a novel device delivery system
Authors: Akihiro Matsumi, Kazuyuki Matsumoto, Daisuke Uchida, Shigeru Horiguchi, Koichiro Tsutsumi, Hironari Kato, Motoyuki Otsuka
Journal: Endoscopy (2023)

The removal of a proximally migrated pancreatic stent is technically challenging [1] [2] [3]. A novel device delivery system (EndoSheather; Piolax) was recently developed, which comprises a slim-tipped guide catheter and pusher tube that facilitate the insertion of devices up to 1.9 mm in diameter [4] [5].
Asthma hospitalisations and heat exposure in England: a case–crossover study during 2002–2019
Authors: Garyfallos Konstantinoudis, Cosetta Minelli, Holly Ching Yu Lam, Elaine Fuertes, Joan Ballester, Bethan Davies, Ana Maria Vicedo-Cabrera, Antonio Gasparrini, Marta Blangiardo
Journal: Thorax (2023)

Previous studies have reported an association between warm temperature and asthma hospitalisation. They have reported different sex-related and age-related vulnerabilities; nevertheless, little is known about how this effect has changed over time and how it varies in space. This study aims to evaluate the association between asthma hospitalisation and warm temperature and investigate vulnerabilities by age, sex, time and space.
High‐Performance Delivery of a CRISPR Interference System via Lipid‐Polymer Hybrid Nanoparticles Combined with Ultrasound‐Mediated Microbubble Destruction for Tumor‐Specific Gene Repression (Adv. Healthcare Mater. 10/2023)
Authors: Yan Li, Pengying Wu, Mingting Zhu, Meiling Liang, Lei Zhang, Yujin Zong, Mingxi Wan
Journal: Advanced Healthcare Materials (2023)

CRISPR Interference Systems The main objective of this study in article 2203082 by Yujin Zong, Mingxi Wan, and co-workers, is to develop novel pH-responsive lipid-polymer hybrid nanoparticles (PLPNs) to achieve optimal CRISPRi system delivery via ultrasound-mediated microbubble destruction (UMMD) technology, thereby inducing efficient target gene repression.
Emerging evidence and treatment paradigm of non-small cell lung cancer
Authors: Si-Yang Maggie Liu, Mei-Mei Zheng, Yi Pan, Si-Yang Liu, Yangqiu Li, Yi-Long Wu
Journal: Journal of Hematology & Oncology (2023)

Abstract Research on biomarker-driven therapy and immune check-point blockade in non-small cell lung cancer (NSCLC) is rapidly evolving. The width and depth of clinical trials have also dramatically improved in an unprecedented speed. The personalized treatment paradigm evolved every year. In this review, we summarize the promising agents that have shifted the treatment paradigm for NSCLC patients across all stages, including targeted therapy and immunotherapy using checkpoint inhibitors. Based on recent evidence, we propose treatment algorithms for NSCLC and propose several unsolved clinical issues, which are being explored in ongoing clinical trials. The results of these trials are likely to impact future clinical practice.
Acidity‐Biodegradable Iridium‐Coordinated Nanosheets for Amplified Ferroptotic Cell Death Through Multiple Regulatory Pathways (Adv. Healthcare Mater. 10/2023)
Authors: Lili Huang, Tongtong Nie, Lixian Jiang, Ying Chen, Yixuan Zhou, Xiaojun Cai, Yuanyi Zheng, Longchen Wang, Jianrong Wu, Tao Ying
Journal: Advanced Healthcare Materials (2023)

Ferroptosis In article 2202562 by Longchen Wang, Jianrong Wu, Tao Ying, and co-workers, an aciditybiodegradable Ir-Hemin nanosheet is presented to achieve notable ferroptosis efficacy through multiple regulatory pathways, including SDT-triggered ROS generation, GPX4 inhibition and HO-1 upregulation-mediated endogenous Fe2+ elevation. This work paves a new way for future studies exploring nanomaterials as ferroptosis inducers.
JBrowse 2: a modular genome browser with views of synteny and structural variation
Authors: Colin Diesh, Garrett J Stevens, Peter Xie, Teresa De Jesus Martinez, Elliot A. Hershberg, Angel Leung, Emma Guo, Shihab Dider, Junjun Zhang, Caroline Bridge, Gregory Hogue, Andrew Duncan, Matthew Morgan, Tia Flores, Benjamin N. Bimber, Robin Haw, Scott Cain, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes
Journal: Genome biology (2023)

Abstract We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.
Overcoming the Stromal Barrier of the Cornea with a Peptide Conjugate Nano‐Assembly to Combat Fungal Keratitis (Adv. Healthcare Mater. 10/2023)
Authors: Xiaoyan Ju, Liping Wu, Ning Gao, Ye Tian, Guojun Lu, Yichen Gao, Shaozhen Zhao, Zhongwei Niu, Ruibo Yang
Journal: Advanced Healthcare Materials (2023)

Fungal Keratitis In article 2202409, Shaozhen Zhao, Zhongwei Niu, Ruibo Yang, and co-workers report a peptide conjugate nano-assembly (PCNA) that permeates corneal stroma and kills the hyphae without irritating the ocular cornea. PCNA with a nano-assembled structure and assembly–disassembly behavior could serve as the foundation of a new therapy for fungal keratitis.
Exploring computer-aided health decision-making on cervical cancer interventions through deliberative interviews in Ethiopia
Authors: Frithjof Sy, Astrid Berner-Rodoreda, Takelech Asnake, Misrak Getnet, Wondwossen Amogne, Hermann Bussmann, Helen Abera, Till Bärnighausen, Andreas Deckert
Journal: npj Digital Medicine (2023)

Cervical cancer is a significant disease burden in Ethiopia. Mathematical models and computer simulations on disease dynamics can support effective resource allocation. The objectives of this work are (i) to explore the perspectives of health decision-makers on computer-aided predictions supporting cervical cancer interventions, (ii) to identify their information needs from these predictions, and (iii) their willingness to apply the results in their work. We conducted deliberative interviews with 15 health decision-makers and advisors in Ethiopia in autumn 2019. We analyze the data using a five steps framework approach drawing on thematic analysis and find that Ethiopian health decision-makers are willing to use computer-aided predictions in their decisions. Data on HPV prevalence and the cervical cancer burden are scarce but valued highly and decision-makers are particularly interested in the identification of local HPV hotspots. Data-driven mathematical models and computer simulations may increasingly influence health decision-making in Ethiopia.
For My Niece, Who Is Thirty-nine Today
Authors: Donna Pucciani
Journal: JAMA (2023)

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